Apples and apple-derived products can be contaminated with patulin and, to a lesser extent, aflatoxin B1 and fumonisins. Fruits were collected from Golden Delicious and Imperatore trees in three orchards in Veneto, Northern Italy, and analysed for the presence of fungi and mycotoxins. Sampling and analyses were also carried out from storage bins to final puree tanks along the apple-puree production chain. Alternaria spp. and Penicillium spp. were commonly isolated from apples collected in the field, but their presence varied with cultivar and orchard location. In contrast, Aspergillus section Flavi spp. and Fusarium spp. were only detected via direct isolation from chopped fruits. Patulin and Alternaria toxins were frequently identified in fresh fruits, while aflatoxins were also present in some fruits albeit at very low levels. Fungi were present in fruits entering the apple-puree production line, but not in apple puree after treatment at 95–105 °C. In contrast, the abovementioned mycotoxins were detected at all stages along the production line. Surprisingly, fumonisins were only detected after the apple puree was subjected to thermal treatment. Implications of these findings were discussed and few unresolved scientific questions were posed to stimulate further lines of study.